It looks like there is a trailing space after sct-umls. Check your ytex.properties file and make sure there is no trailing space after the ytex.conceptGraphName property value
On Wed, Nov 5, 2014 at 8:35 PM, Natalia Connolly < [email protected]> wrote: > Well, it't not really an error - ytex runs fine, it's just that the word > sense disambiguation remains disabled without conceptGraph, and I really > need it. Here's the full log of the initialization step, with the relevant > parts highlighted in yellow: > > >bin/runctakesCPE.sh > Nov 5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM: invalid > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] <Error>: CGContextGetCTM: invalid > context 0x0 > Nov 5 14:27:33 P13-7415 java[15257] <Error>: CGContextSetBaseCTM: invalid > context 0x0 > log4j: reset attribute= "false". > log4j: Threshold ="null". > log4j: Level value for root is [INFO]. > log4j: root level set to INFO > log4j: Class name: [org.apache.log4j.ConsoleAppender] > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" > log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} > %5p %c{1} - %m%n]. > log4j: Adding appender named [consoleAppender] to category [root]. > 05 Nov 2014 14:27:34 INFO ClearNLPDependencyParserAE - using Morphy > analysis? true > Loading configuration. > Loading feature templates. > Loading lexica. > Loading model: > > ........................................................................................ > 05 Nov 2014 14:27:48 INFO TokenizerAnnotatorPTB - Initializing > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > 05 Nov 2014 14:27:48 INFO ContextDependentTokenizerAnnotator - Finite > state machines loaded. > 05 Nov 2014 14:27:48 INFO ContextAnnotator - SCOPE ORDER: [1, 3] > 05 Nov 2014 14:27:49 INFO StatusContextAnalyzer - initBoundaryData() > called for ContextInitializer > 05 Nov 2014 14:27:49 INFO ContextAnnotator - SCOPE ORDER: [1, 3] > 05 Nov 2014 14:27:49 INFO NegationContextAnalyzer - initBoundaryData() > called for ContextInitializer > 05 Nov 2014 14:27:49 INFO ApplicationContextHolder - loading > ytex.properties from: > file:/usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/ytex.properties > 05 Nov 2014 14:27:49 INFO ApplicationContextHolder - > beanRefContext=classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml > 05 Nov 2014 14:27:49 INFO ClassPathXmlApplicationContext - Refreshing > org.springframework.context.support.ClassPathXmlApplicationContext@3a9d23c0: > startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Overriding bean > definition for bean 'ytexApplicationContext': replacing [Generic bean: > class [org.springframework.context.support.ClassPathXmlApplicationContext]; > scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; > autowireCandidate=true; primary=false; factoryBeanName=null; > factoryMethodName=null; initMethodName=null; destroyMethodName=null; > defined in URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-res-3.2.0.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] > with [Generic bean: class > [org.springframework.context.support.ClassPathXmlApplicationContext]; > scope=; abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0; > autowireCandidate=true; primary=false; factoryBeanName=null; > factoryMethodName=null; initMethodName=null; destroyMethodName=null; > defined in URL > [jar:file:/usr/local/apache-ctakes-3.2.0/lib/ctakes-ytex-web-3.2.0-classes.jar!/org/apache/ctakes/ytex/uima/beanRefContext.xml]] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Pre-instantiating > singletons in > org.springframework.beans.factory.support.DefaultListableBeanFactory@271d5641: > defining beans [ytexApplicationContext]; root of factory hierarchy > 05 Nov 2014 14:27:49 INFO ClassPathXmlApplicationContext - Refreshing > org.springframework.context.support.ClassPathXmlApplicationContext@4183422d: > startup date [Wed Nov 05 14:27:49 EST 2014]; root of context hierarchy > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-datasource.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-kernel.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/beans-kernel-sim.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima.hbm.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima-dao.xml] > 05 Nov 2014 14:27:49 INFO XmlBeanDefinitionReader - Loading XML bean > definitions from class path resource > [org/apache/ctakes/ytex/uima/beans-uima-mapper.xml] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Overriding bean > definition for bean 'mapperOperation': replacing [Root bean: class > [org.springframework.aop.aspectj.AspectJExpressionPointcut]; > scope=prototype; abstract=false; lazyInit=false; autowireMode=0; > dependencyCheck=0; autowireCandidate=true; primary=false; > factoryBeanName=null; factoryMethodName=null; initMethodName=null; > destroyMethodName=null] with [Root bean: class > [org.springframework.aop.aspectj.AspectJExpressionPointcut]; > scope=prototype; abstract=false; lazyInit=false; autowireMode=0; > dependencyCheck=0; autowireCandidate=true; primary=false; > factoryBeanName=null; factoryMethodName=null; initMethodName=null; > destroyMethodName=null] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex-default.properties] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex.properties] > 05 Nov 2014 14:27:49 INFO PropertyPlaceholderConfigurer - Loading > properties file from class path resource > [org/apache/ctakes/ytex/ytex-umls.properties] > 05 Nov 2014 14:27:49 INFO DefaultListableBeanFactory - Pre-instantiating > singletons in > org.springframework.beans.factory.support.DefaultListableBeanFactory@26df536f: > defining beans > [org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator,sessionFactory,ytexDaoOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#8,documentDao,namedEntityRegexDao,segmentRegexDao,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#9,ISO8601Converter,documentMapperService]; > root of factory hierarchy > 05 Nov 2014 14:27:49 INFO PropertiesFactoryBean - Loading properties file > from class path resource [org/apache/ctakes/ytex/ytex.properties] > 05 Nov 2014 14:27:50 INFO Version - HCANN000001: Hibernate Commons > Annotations {4.0.2.Final} > 05 Nov 2014 14:27:50 INFO Version - HHH000412: Hibernate Core > {4.2.6.Final} > 05 Nov 2014 14:27:50 INFO Environment - HHH000206: hibernate.properties > not found > 05 Nov 2014 14:27:50 INFO Environment - HHH000021: Bytecode provider name > : javassist > 05 Nov 2014 14:27:51 INFO Dialect - HHH000400: Using dialect: > org.hibernate.dialect.MySQLMyISAMDialect > 05 Nov 2014 14:27:51 WARN RootClass - HHH000038: Composite-id class does > not override equals(): > org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink > 05 Nov 2014 14:27:51 WARN RootClass - HHH000039: Composite-id class does > not override hashCode(): > org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink > 05 Nov 2014 14:27:51 INFO TransactionFactoryInitiator - HHH000399: Using > default transaction strategy (direct JDBC transactions) > 05 Nov 2014 14:27:51 INFO ASTQueryTranslatorFactory - HHH000397: Using > ASTQueryTranslatorFactory > 05 Nov 2014 14:27:51 INFO UpdateTimestampsCache - HHH000250: Starting > update timestamps cache at region: > org.hibernate.cache.spi.UpdateTimestampsCache > 05 Nov 2014 14:27:51 INFO StandardQueryCache - HHH000248: Starting query > cache at region: org.hibernate.cache.internal.StandardQueryCache > 05 Nov 2014 14:27:51 INFO TableGenerator - HHH000398: Explicit segment > value for id generator [ytex.hibernate_sequences.sequence_name] suggested; > using default [default] > 05 Nov 2014 14:27:51 WARN AbstractEhcacheRegionFactory - HHH020003: Could > not find a specific ehcache configuration for cache named > [org.apache.ctakes.ytex.uima.model.UimaType]; using defaults. > 05 Nov 2014 14:27:51 WARN EhcacheAccessStrategyFactoryImpl - HHH020007: > read-only cache configured for mutable entity > [org.apache.ctakes.ytex.uima.model.UimaType] > 05 Nov 2014 14:27:52 INFO HibernateTransactionManager - Using DataSource > [org.apache.commons.dbcp.BasicDataSource@2fbd46ab] of Hibernate > SessionFactory for HibernateTransactionManager > 05 Nov 2014 14:27:52 INFO EhCacheManagerFactoryBean - Initializing > EHCache CacheManager > 05 Nov 2014 14:27:52 WARN CacheManager - Creating a new instance of > CacheManager using the diskStorePath > "/var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T/" which is already used > by an existing CacheManager. > The source of the configuration was > net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@6485a56f. > The diskStore path for this CacheManager will be set to > /var/folders/2z/n9b16tpn2f35tk85nx_hjbrhbyn5c4/T//ehcache_auto_created_1415215672746. > To avoid this warning consider using the CacheManager factory methods to > create a singleton CacheManager or specifying a separate ehcache > configuration (ehcache.xml) for each CacheManager instance. > 05 Nov 2014 14:27:53 INFO ConceptSimilarityServiceImpl - begin > initialization for concept graph: sct-umls > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - could not load conceptGraph > from classpath, attempt to load from: > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls > .gz > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - > /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls > .gz not found, cannot load concept graph > 05 Nov 2014 14:27:53 INFO ConceptDaoImpl - could not load conceptGraph: > sct-umls > 05 Nov 2014 14:27:53 WARN ConceptSimilarityServiceImpl - concept graph > null, name: sct-umls > 05 Nov 2014 14:27:53 INFO ConceptSimilarityServiceImpl - end > initialization for concept graph: sct-umls > 05 Nov 2014 14:27:53 INFO Dialect - HHH000400: Using dialect: > org.hibernate.dialect.MySQLMyISAMDialect > 05 Nov 2014 14:27:53 INFO DocumentMapperServiceImpl - document table name > = ytex.document > 05 Nov 2014 14:27:53 INFO SentenceDetector - [SegmentsToSkip, > SentenceModelFile] > 05 Nov 2014 14:27:53 INFO SentenceDetector - Sentence detector model > file: org/apache/ctakes/core/sentdetect/sd-med-model.zip > 05 Nov 2014 14:27:53 WARN SenseDisambiguatorAnnotator - Concept Graph was > not loaded - word sense disambiguation disabled > 05 Nov 2014 14:27:53 INFO POSTagger - POS tagger model file: > org/apache/ctakes/postagger/models/mayo-pos.zip > Loading configuration. > > > On Wed, Nov 5, 2014 at 2:05 PM, vijay garla <[email protected]> wrote: > >> can you send the full stack trace of the error? Please pipe the output >> and stderr to a file >> >> On Wed, Nov 5, 2014 at 8:03 PM, Natalia Connolly < >> [email protected]> wrote: >> >>> Yes, I did the step and I do see that file in >>> resources/org/apache/ctakes/ytex/conceptGraph. >>> >>> On Wed, Nov 5, 2014 at 1:59 PM, vijay garla <[email protected]> wrote: >>> >>>> did you do this part (see below). If so, you should see the file >>>> sct-umls.gz in resources/org/apache/ctakes/ytex/conceptGraph/ >>>> >>>> >>>> 3) Unzip YTEX Resources (Optional - UTS login required) >>>> >>>> Download and unzip ctakes-ytex-resources-3.1.2-SNAPSHOT.zip >>>> <http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip> >>>> 'over' >>>> your installation. This contains: >>>> >>>> - Concept Graphs derived from the UMLS2013AA used to compute >>>> semantic similarity measures >>>> - Dictionary Lookup table derived from UMLS2013AA for named entity >>>> recognition. >>>> >>>> >>>> On Wed, Nov 5, 2014 at 6:01 PM, Natalia Connolly < >>>> [email protected]> wrote: >>>> >>>>> Hi All, >>>>> >>>>> I'm trying out ytex within cTAKES 3.2. I followed all the >>>>> instructions listed here : >>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation, >>>>> and I verified that the setup was fine (from setup.out). >>>>> >>>>> My ytex.properties file contains the line: >>>>> >>>>> ytex.conceptGraphName=sct-umls >>>>> >>>>> and I do have sct-umls.xml in my >>>>> ${CTAKES_HOME}/resources/org/apache/ctakes/ytex/conceptGraph. >>>>> >>>>> Despite all this I can't seem to get conceptGraph working. The >>>>> error message is the following: >>>>> >>>>> 05 Nov 2014 11:56:31 INFO ConceptSimilarityServiceImpl - begin >>>>> initialization for concept graph: sct-umls >>>>> 05 Nov 2014 11:56:31 INFO ConceptDaoImpl - could not load >>>>> conceptGraph from classpath, attempt to load from: >>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls >>>>> .gz >>>>> 05 Nov 2014 11:56:31 INFO ConceptDaoImpl - >>>>> /usr/local/apache-ctakes-3.2.0/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls >>>>> .gz not found, cannot load concept graph >>>>> >>>>> I don't understand what needs to go into CLASSPATH to indicate >>>>> where conceptGraph is, as it already contains ${CTAKES_HOME}/resources. >>>>> My >>>>> class path is set according to the documentation to: >>>>> >>>>> ${CTAKES_HOME}/desc:/${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/* >>>>> >>>>> Any help would be appreciated. >>>>> >>>>> Natalia >>>>> >>>>> >>>>> >>>>> >>>> >>> >> >
